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Yorodumi- PDB-1zq7: X-Ray Crystal Structure of Protein Q8PZK8 from Methanosarcina maz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zq7 | ||||||
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Title | X-Ray Crystal Structure of Protein Q8PZK8 from Methanosarcina mazei. Northeast Structural Genomics Consortium Target MaR9. | ||||||
Components | Hypothetical protein MM0484 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / MAR9 / Q8PZK8 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information Hypothetical protein ph0010; domain 2 / Hypothetical protein ph0010; domain 1 / AMMECR1 domain / Uncharacterised protein family MJ0810 / AMMECR1 / AMMECR1, N-terminal / AmmeMemoRadiSam system protein A / AMMECR1 domain superfamily / AMMECR1 / AMMECR1 domain profile. ...Hypothetical protein ph0010; domain 2 / Hypothetical protein ph0010; domain 1 / AMMECR1 domain / Uncharacterised protein family MJ0810 / AMMECR1 / AMMECR1, N-terminal / AmmeMemoRadiSam system protein A / AMMECR1 domain superfamily / AMMECR1 / AMMECR1 domain profile. / Glycoprotein, Type 4 Pilin / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.11 Å | ||||||
Authors | Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Yong, W. / Xiao, R. / Ma, L.-C. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-Ray structure of the hypothetical protein Q8PZK8 from Methanosarcina mazei at the resolution 2.1A. Northeast Structural Genomics Consortium target MaR9. Authors: Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Yong, W. / Xiao, R. / Ma, L.-C. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zq7.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zq7.ent.gz | 138.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zq7_validation.pdf.gz | 452.5 KB | Display | wwPDB validaton report |
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Full document | 1zq7_full_validation.pdf.gz | 468.8 KB | Display | |
Data in XML | 1zq7_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 1zq7_validation.cif.gz | 47 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/1zq7 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/1zq7 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23191.809 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PZK8 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.336 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 200 mM ammonium sulfate, 18% PEG 3350, 50 Nm Hepes, 3% 1,3 Butanedio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97902, 0.97924, 0.96788 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 6, 2005 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→30 Å / Num. obs: 76303 / % possible obs: 89.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 2.53 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.2 | ||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 78.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.11→29.83 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 455557.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.7008 Å2 / ksol: 0.367839 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 24.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.11→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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